Abstract: In the report， a numerical model was established based on the VRANS equation， and the surface layer of coral reef was simplified as a porous medium with constant porosity. The effects of the different incident wave periods and wave heights in the coral reef topography with lagoons on the wave height and water level enhancement on the reef flat and in the lagoon were simulated and analyzed. The results showed that after the regular wave breaks， the wave decreases obviously on the reef flat， and under the action of porous medium， the most obvious position of water enhancement effect is near the reef edge on the reef flat， the larger the wave height and period， the larger the wave and water level in the reef flat and lagoon. The results provide an explanation for the study of wave deformation and water setup on the porous reef， and set a reference for the analysis of the causes of failure and damage of structures on the reef flat.